Standard fit report for fits of hierSCAL to DERPA data.
Data Scenario: 1956_allFleets
Model Hypothesis: baseModel
Species: Dover, English, Rock
Stocks: HSHG, QCS, WCVI
Max Gradient: 0.0448653
Objective Function value: -1286.0359798
Time to fit model: 19.5005167
Figure 1: Spawning biomass (red line), catch (grey bars), and scaled biomass indices (coloured points), for all stocks and species. Indices are scaled by the fleet catchability, then by the ratio of spawning biomass to vulnerable biomass.
Figure 2: Standardised vulnerable biomass (coloured lines) and the scaled and standardised biomass indices they are fitting to (coloured points), for all stocks and species.
Figure 3: Standardised residuals for model fits to biomass indices (coloured points) and a loess smoother with a 20% confidence interval (coloured lines and grey regions), for all fleets, stocks, and species.
Figure 4: Age-1 recruitments for all species and stocks. Equilibrium unfished recruitment \(R_0\) is indicated by the horizontal dashed line.
Figure 5: Deviations from expected recruitment for all species and stocks.
Figure 6: Stock-recruit curves (solid lines) and modeled recruitments (grey points), gridded over species (columns) and stocks (rows).
Figure 7: Estimates of fishing mortality from each fleet (coloured points and lines), gridded over species (columns) and stocks (rows). Fishing mortality rates are found using an iterative Newton-Rhapson solver conditioned on the observed catch.
Figure 8: Modeled removals (blue points) using estimated fishing mortality compared to observed catches (open circles), gridded over species (columns) and stocks (rows).
Figure 9: Probability curves of length-at-age for males (blue) and females (red). Curves show the probability of each length within an age group, and opacity of the lines increases with age.
Figure 10: Selectivity-at-length for each fleet, gridded over species (columns) and stocks (rows).
Figure 11: Selectivity-at-age for each fleet, for females only, gridded over species (columns) and stocks (rows).
Figure 12: Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the modern trawl fleet.
Re-read Hilborn 2018 for the goldilocks plot
| Species | Stock | B0 | R0 | M_m | M_f | h | Bmsy | Fmsy | Umsy | MSY | SSB_T | D_T | Dmsy_T |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Dover | HSHG | 17.46 | 3.14 | 0.13 | 0.08 | 0.77 | 6.04 | 0.19 | 0.17 | 0.64 | 6.01 | 0.34 | 1 |
| Dover | QCS | 5.94 | 1.21 | 0.14 | 0.09 | 0.77 | 1.97 | 0.17 | 0.15 | 0.23 | 1.69 | 0.28 | 0.86 |
| Dover | WCVI | 15.15 | 4.59 | 0.17 | 0.11 | 0.77 | 5 | 0.21 | 0.19 | 0.71 | 3.98 | 0.26 | 0.8 |
| English | HSHG | 9.98 | 4.78 | 0.16 | 0.12 | 0.79 | 3.42 | 0.37 | 0.32 | 0.69 | 6.01 | 0.6 | 1.76 |
| English | QCS | 0.57 | 0.32 | 0.19 | 0.14 | 0.8 | 0.19 | 0.34 | 0.29 | 0.04 | 0.38 | 0.67 | 2 |
| English | WCVI | 0.9 | 0.47 | 0.18 | 0.13 | 0.8 | 0.3 | 0.34 | 0.29 | 0.07 | 0.37 | 0.41 | 1.23 |
| Rock | HSHG | 16.34 | 5.54 | 0.25 | 0.17 | 0.75 | 5.75 | 0.27 | 0.23 | 0.83 | 8.46 | 0.52 | 1.47 |
| Rock | QCS | 5.55 | 1.57 | 0.23 | 0.15 | 0.76 | 1.89 | 0.24 | 0.21 | 0.3 | 1.61 | 0.29 | 0.85 |
| Rock | WCVI | 1.72 | 0.38 | 0.2 | 0.14 | 0.74 | 0.63 | 0.26 | 0.23 | 0.08 | 0.7 | 0.41 | 1.11 |
Figure 13: Standardised recruitment deviations. Blue indicates a positive deviation, red indicates a negative deviation, and the area of each circle is proportional to the size of the deviation.
UNDER CONSTRUCTION
| phase | objFun | maxGrad | nPar | convCode | convMsg | time | mcmcTime |
|---|---|---|---|---|---|---|---|
| 1 | 1005.5757 | 0.0000539 | 33 | 0 | relative convergence (4) | 0.4234000 | NA |
| 2 | -285.7490 | 0.0018599 | 42 | 0 | relative convergence (4) | 1.0169833 | NA |
| 3 | -288.1209 | 0.0048975 | 44 | 0 | relative convergence (4) | 0.9178667 | NA |
| 4 | -565.3093 | 0.0021900 | 404 | 0 | relative convergence (4) | 1.0744667 | NA |
| 5 | -571.1965 | 0.0424105 | 413 | 0 | relative convergence (4) | 1.7255167 | NA |
| 6 | -571.6236 | 0.0451117 | 422 | 0 | relative convergence (4) | 2.3463500 | NA |
| 7 | -640.5282 | 0.0301879 | 425 | 0 | relative convergence (4) | 2.8796667 | NA |
| 8 | -750.0643 | 0.0630976 | 431 | 0 | relative convergence (4) | 2.4864167 | NA |
| 9 | -1264.0039 | 0.0573926 | 454 | 0 | relative convergence (4) | 2.4073167 | NA |
| 10 | -1264.0039 | 0.0008141 | 454 | 0 | relative convergence (4) | 1.5402167 | NA |
| 11 | -1286.0360 | 0.0448653 | 475 | 0 | relative convergence (4) | 2.6823167 | NA |
| RE | NA | NA | NA | NA | NA | NA | NA |